In Vivo Tracking of Hematopoietic Stem and Progenitor Cell Ontogeny by Cellular Barcoding

Tak, Tamar; Eisele, Almut; Perié, Leïla

doi:10.1007/978-1-0716-1425-9_21

Cited by 2 publications

(3 citation statements)

References 12 publications

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“…The barcode library used consists of 98 bp semi-random DNA fragments in the 3’ UTR of a GFP cassette as described by ( 45 ) and described in detail elsewhere ( 46 ). The barcode reference list is available on https://github.com/TeamPerie/HadjAbed-et-al._2022 .…”

Section: Methodsmentioning

confidence: 99%

“…Barcodes were amplified as published previously ( 46 ). In short, lysed cell preparations were split to allow for duplicate measurements.…”

Section: Methodsmentioning

confidence: 99%

“…The barcode library used consists of 98 bp semi-random DNA fragments in the 3' UTR of a GFP cassette as described by (45) and described in detail elsewhere (46)…”

Section: Barcode Library Barcode Reference Listmentioning

confidence: 99%

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CellDestiny: A RShiny application for the visualization and analysis of single-cell lineage tracing data

et al. 2022

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Single-cell lineage tracing permits the labeling of individual cells with a heritable marker to follow the fate of each cell’s progeny. Over the last twenty years, several single-cell lineage tracing methods have emerged, enabling major discoveries in developmental biology, oncology and gene therapies. Analytical tools are needed to draw meaningful conclusions from lineage tracing measurements, which are characterized by high variability, sparsity and technical noise. However, the single cell lineage tracing field lacks versatile and easy-to-use tools for standardized and reproducible analyses, in particular tools accessible to biologists. Here we present CellDestiny, a RShiny app and associated web application developed for experimentalists without coding skills to perform visualization and analysis of single cell lineage-tracing datasets through a graphical user interface. We demonstrate the functionality of CellDestiny through the analysis of (i) lentiviral barcoding datasets of murine hematopoietic progenitors; (ii) published integration site data from Wiskott-Aldrich Symdrome patients undergoing gene-therapy treatment; and (iii) simultaneous barcoding and transcriptomic analysis of murine hematopoietic progenitor differentiation in vitro. In summary, CellDestiny is an easy-to-use and versatile toolkit that enables biologists to visualize and analyze single-cell lineage tracing data.

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Section: Methodsmentioning

confidence: 99%

“…Barcodes were amplified as published previously ( 46 ). In short, lysed cell preparations were split to allow for duplicate measurements.…”

Section: Methodsmentioning

confidence: 99%

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CellDestiny: A RShiny application for the visualization and analysis of single-cell lineage tracing data

et al. 2022

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Single Cell Transcriptomics to Understand HSC Heterogeneity and Its Evolution upon Aging

Hérault

Poplineau

Rémy

et al. 2022

Cells

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Single-cell transcriptomic technologies enable the uncovering and characterization of cellular heterogeneity and pave the way for studies aiming at understanding the origin and consequences of it. The hematopoietic system is in essence a very well adapted model system to benefit from this technological advance because it is characterized by different cellular states. Each cellular state, and its interconnection, may be defined by a specific location in the global transcriptional landscape sustained by a complex regulatory network. This transcriptomic signature is not fixed and evolved over time to give rise to less efficient hematopoietic stem cells (HSC), leading to a well-documented hematopoietic aging. Here, we review the advance of single-cell transcriptomic approaches for the understanding of HSC heterogeneity to grasp HSC deregulations upon aging. We also discuss the new bioinformatics tools developed for the analysis of the resulting large and complex datasets. Finally, since hematopoiesis is driven by fine-tuned and complex networks that must be interconnected to each other, we highlight how mathematical modeling is beneficial for doing such interconnection between multilayered information and to predict how HSC behave while aging.

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In Vivo Tracking of Hematopoietic Stem and Progenitor Cell Ontogeny by Cellular Barcoding

Cited by 2 publications

References 12 publications

CellDestiny: A RShiny application for the visualization and analysis of single-cell lineage tracing data

CellDestiny: A RShiny application for the visualization and analysis of single-cell lineage tracing data

Single Cell Transcriptomics to Understand HSC Heterogeneity and Its Evolution upon Aging

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